Genome Assembly of Alfalfa Cultivar Zhongmu-4 and Identification of SNPs Associated with Agronomic Traits  

作　　者：Ruicai Long Fan Zhang Zhiwu Zhang Mingna Li Lin Chen Xue Wang Wenwen Liu Tiejun Zhang Long-Xi Yu Fei He Xueqian Jiang Xijiang Yang Changfu Yang Zhen Wang Junmei Kang Qingchuan Yang 

机构地区：[1]Institute of Animal Sciences,Chinese Academy of Agricultural Sciences,Beijing 100193,China [2]Department of Crop and Soil Sciences,Washington State University,Pullman,WA 99163,USA [3]School of Grassland Science,Beijing Forestry University,Beijing 100083,China [4]United States Department of Agriculture-Agricultural Research Service,Plant and Germplasm Introduction and Testing Research,Prosser,WA 99350,USA

出　　处：《Genomics, Proteomics & Bioinformatics》2022年第1期14-28,共15页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(Grant Nos.31971758 to QY and 32071865 to RL);the Collaborative Research Key Project between China and EU(Grant No.2017YFE0111000);the China Agriculture Research System of MOF and MARA(Grant No.CARS-34);the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(Grant No.ASTIP-IAS14);the Key Projects in Science and Technology of Inner Mongolia,China(Grant No.2021ZD0031)。

摘　　要：Alfalfa(Medicago sativa L.)is the most important legume forage crop worldwide with high nutritional value and yield.For a long time,the breeding of alfalfa was hampered by lacking reliable information on the autotetraploid genome and molecular markers linked to important agronomic traits.We herein reported the de novo assembly of the allele-aware chromosome-level genome of Zhongmu-4,a cultivar widely cultivated in China,and a comprehensive database of genomic variations based on resequencing of 220 germplasms.Approximate 2.74 Gb contigs(N50 of 2.06 Mb),accounting for 88.39%of the estimated genome,were assembled,and 2.56 Gb contigs were anchored to 32 pseudo-chromosomes.A total of 34,922 allelic genes were identified from the allele-aware genome.We observed the expansion of gene families,especially those related to the nitrogen metabolism,and the increase of repetitive elements including transposable elements,which probably resulted in the increase of Zhongmu-4 genome compared with Medicago truncatula.Population structure analysis revealed that the accessions from Asia and South America had relatively lower genetic diversity than those from Europe,suggesting that geography may influence alfalfa genetic divergence during local adaption.Genome-wide association studies identified 101 single nucleotide polymorphisms(SNPs)associated with 27 agronomic traits.Two candidate genes were predicted to be correlated with fall dormancy and salt response.We believe that the alleleaware chromosome-level genome sequence of Zhongmu-4 combined with the resequencing data of the diverse alfalfa germplasms will facilitate genetic research and genomics-assisted breeding in variety improvement of alfalfa.

关 键 词：ALFALFA AUTOTETRAPLOID Genome assembly RESEQUENCING Genome-wide association study 

分 类 号：S541.9[农业科学—作物学]